Marine protected areas (MPAs) have proliferated in the past decades to protect biodiversity and sustain fisheries. However, most of the MPA networks have been designed without taking into account a critical factor: the larval dispersal patterns of populations within and outside the reserves. The scale and predictability of larval dispersal, however, remain unknown due to the difficulty of measuring dispersal when larvae are minute (~ cm) compared to the potential scale of dispersal (~ km). Nevertheless, genetic approaches can now be used to make estimates of larval dispersal. The following thesis describes self-recruitment and connectivity patterns of a coral reef fish species (Centropyge bicolor) in Kimbe Bay, Papua New Guinea. To do this, microsatellite markers were developed to evaluate fine-scale genetics and recruit assignment via genetic parentage analysis. In this method, offspring are assigned to potential parents, so that larval dispersal distances can then be inferred for each individual larvae. From a total of 255 adults and 426 juveniles collected only 2 parentoffspring pairs were assigned, representing less than 1% self-recruitment. Previous data from the same study system showed that both Chaetodon vagagundus and Amphiprion percula have consistent high self-recuitment rates (~ 60%), despite having contrasting life history traits. Since C. bicolor and C. vagabundus have similar characteristics (e.g. reproductive mode, pelagic larval duration), comparable results were expected. On the contrary, the results of this study showed that dispersal patterns cannot be generalized across species. Hence the importance of studying different species and seascapes to better understand the patterns of larval dispersal. This, in turn, will be essential to improve the design and implementation of MPAs as conservation and management tools.

Knowledge in the spatial patterns of fish larval dispersal is crucial for the establishment of a sustainable management of fisheries and species conservation. Direct quantification of larval dispersal is a challenging task due to the difficulty associated with larval tracking in the vast ocean. However, genetic approaches can be used to estimate it. Here, I employed genetic markers (microsatellites) as a proxy to determine dispersal patterns and self-recruitment levels using parentage analysis in the bumphead parrotfish (Bolbometapon muricatum) in the Solomon Islands. Tissue samples of 3924 fish (1692 juveniles, 1121 males and 1111 females) were collected from a spear-fishery at the Kia District in Santa Isabel Island. The samples come from three distinct zones with different fishing pressure histories (lightly fished, recently fished, and heavily fished). The mean dispersal distance estimated for the bumphead parrotfish was 36.5 Km (range 4 – 78 Km) and the genetic diversity for the population studied was low in comparison with other reef fishes. The parentage analysis identified 68 parent–offspring relationships, which represents a self-recruitment level of almost 50 %. Most of the recruits were produced in the zone that recently started to be fished and most of these recruits dispersed to the heavily fished zone. Comparisons of genetic diversity and relatedness among adults and juveniles suggested the potential occurrence of sweepstakes reproductive success. These results suggest that management measures must be taken straightaway to assure the sustainability of the spear-fishery. These measures may imply the ban on juveniles fishing in the heavily fished zone and the larger adults in the recently fished zone. Overall, the population dynamics of the studied system seem to be strongly shaped by self-recruitment and sweepstakes reproduction events.

With a dramatic decrease of biodiversity as a result of the increase in exploitation of marine ecosystems, the establishment of marine protected areas (MPAs) serves as an important means of protecting those resources. Although there is support for the effectiveness of these MPAs and MPA networks, there is room for improvement in terms of MPA management and design. For example, a better understanding of the dispersal dynamics of targeted species across these MPAs will serve as a more accurate means of reserve as well as fisheries management. While there have been many methods used to determine the larval dispersal of a certain species, parentage analysis is becoming the most robust. In this thesis, I attempt to determine the patterns of self-recruitment and larval dispersal of the Longfin Grouper (Epinephelus quoyanus) in one focal marine reserve within the Great Keppel Island group through the method of parentage. For this, I developed 14 microsatellite markers and with those, genotyped 610 adults as well as 478 juveniles from the study site. These genotypes allowed me to assign offspring to their potential parents, which then allowed me to measure the self-recruitment, local retention as well as larval dispersal percentages of this species from and within the reserve. My results indicate that there is 32% local retention to the reserve while 68% of the assigned juveniles were dispersed to other areas (4% of which dispersed to another reserve). Previous studies conducted in the same area showed higher reserve self-recruitment rates for both Plectropomus maculatus (~30%) and Lutjanus carponotatus (64%) despite their similar life history traits. The results from this study add to the growing evidence that dispersal patterns cannot be generalized across marine systems or even between species within a single system.

The field of marine population connectivity is receiving growing attention from ecologists worldwide. The degree to which metapopulations are connected via larval dispersal has vital ramifications for demographic and evolutionary dynamics and largely determines the way we manage threatened coastal ecosystems. Here we addressed different questions relating to connectivity by integrating direct and indirect genetic approaches over different spatial and ecological scales in a coral reef fish in the Red Sea. We developed 35 novel microsatellite loci for our study organism the two-band anemonefish Amphiprion bicinctus (Rüppel 1830), which served as the basis of the following approaches. First, we collected nearly one thousand samples of A. bicinctus from 19 locations across 1500 km along the Saudi Arabian coast to infer population genetic structure. Genetic variability along the northern and central coast was weak, but showed a significant break at approximately 20°N. Implementing a model of isolation by environment with chlorophyll-a concentrations and geographic distance as predictors we were able to explain over 90% of the genetic variability in the data (R2 = 0.92). For the second approach we sampled 311 (c. 99%) putative parents and 172 juveniles at an isolated reef, Quita al Girsh (QG), to estimate self-recruitment using genetic parentage analysis. Additionally we collected 176 juveniles at surrounding locations to estimate larval dispersal from QG and ran a biophysical dispersal model of the system with real5 time climatological forcing. In concordance with model predictions, we found a complete lack (c. 0.5%) of self-recruitment over two sampling periods within our study system, thus presenting the first empirical evidence for a largely open reef fish population. Lastly, to conceptualize different hypotheses regarding the underlying processes and mechanisms of self-recruitment versus long-distance dispersal in marine organisms with pelagic larval stages, I introduce and discuss the concept of “origin effects”, providing the theoretical background to some of the questions that have arisen during this research. Overall, this thesis has generated significant new insights into the patterns of coral reef fish connectivity, specifically for the Red Sea, where such information has previously been scarce.

L’érosion des stocks naturels de Paracentrotus lividus, oursins comestibles de Méditerranée, malgré les mesures actuelles réglementant les captures, soulève des inquiétudes sur la pérennité de son exploitation et sur l'équilibre des écosystèmes. En 2009, à la demande des pêcheurs professionnels, des gestionnaires de la ressource et de la communauté d’agglomération Toulon Provence Méditerranée (TPM), l'Institut Océanographique Paul Ricard et l'Équipe de Biologie Moléculaire Marine du laboratoire PROTEE (Université de Toulon), ont engagé un travail de recherche visant à mieux comprendre l'influence des processus naturels et anthropiques qui façonnent les populations naturelles, dans le but d'améliorer les stratégies de soutien aux populations, notamment par le réensemencement de juvéniles d'oursins.L'objectif du travail de thèse a été de (i) caractériser l'état des stocks sauvages de l'aire toulonnaise et de leurs dynamiques par la mise en place du suivi démographique bisannuel à long terme de huit stations références, (ii) de développer les méthodes de production de juvéniles en écloserie et (iii) d'évaluer l'efficacité du repeuplement et son impact sur les populations naturelles. Compte-tenu du cycle de vie bentho-pélagique de P. lividus, nous avons inscrit cette problématique dans une échelle régionale.Les résultats obtenus permettent de dresser un premier état des lieux de la structuration et des fluctuations d'abondances des peuplements de P. lividus sur l'aire toulonnaise et démontrent la fragilité des stocks naturels vis à vis des captures. La maîtrise complète du cycle de vie en aquaculture a été obtenue, notamment en optimisant les conditions d’élevage au stade critique de la métamorphose. Enfin, les repeuplements expérimentaux, réalisés à l'échelle pilote, ont présenté un succès variable selon les sites mais potentiellement important, sans aucun effet sur la structuration et la diversité génétique des stocks naturels. Le travail engagé et les premiers résultats sont discutés dans le contexte de la conservation et de l'exploitation durable de cette ressource naturelle. Ils constituent en outre un préalable indispensable aux réflexions sur l’ajustement ou la mise en place de nouvelles actions de gestion des populations et de la ressource. / Despite current measures regulating captures, the erosion of natural stocks of the edible Paracentrotus lividus sea urchin of Mediterranean Sea, raises concerns about the sustainability of its exploitation and the stability of the associated ecosystem. In 2009, upon request of professional fishermen, resource managers and the urban district of Toulon Provence Méditerranée, we have initiated a program of research to better understand the influence of natural and anthropogenic processes that shape natural populations. The objectives of the thesis were (1) to monitor the demographic evolution of P. lividus communities on eight sites of the Toulon area between 2011 and 2013 before and after the legal harvesting period, (2) to develop a reliable method of production of P. lividus juveniles in hatchery and (3) to evaluate the effectiveness of restocking at a pilot scale and assess its potential impact over natural populations. Given the long larval phase in the bentho-pelagic cycle of this species, we monitored the genetic diversity of P. lividus populations at a regional scale.The data and results acquired during this work first provide an initial evaluation of the structure, abundance and fluctuation of followed P. lividus populations along the Toulon coast and demonstrate the vulnerability of natural stocks towards harvesting. In addition, complete control over the whole life cycle in batch was achieved through optimization of cultural and food parameters, especially at the critical stage of settlement and metamorphosis. Finally, experimental restocking trials demonstrated varying success depending on the site, but potentially significant, without apparent effect on the genetic diversity of wild stocks. Results obtained in this thesis are discussed in the context of conservation and sustainable exploitation of this natural resource. They are also a prerequisite to discussion on the adjustment or implementation of new management guidelines.

Palms are ecologically important and charismatic trees of the tropics. They are important to the livelihood of local communities and are key resources for the frugivore community in tropical forests. These frugivores are in turn hunted by humans for food. This ecological connection between human, palms, and frugivores provides a unique setting to study how cultural and ecological components within this multitrophic interaction influences palm populations. In chapter 1, I explored the traditional and ecological knowledge behind the cultivation of palm-weevil larvae for food. I found the Joti people, cultivated two species of weevil-larvae differently, which also determined whether palms were logged before or after reproductive maturity. The cultivation of each weevil-larvae species therefore had a differential impact on palm populations. In chapter 2, I investigated how frugivores mediate interactions between two dominant and co-occuring palms in the Peruvian Amazonia-- Attalea phalerata and Astrocaryum murumuru. I found frugivores codispersed seeds of the two palm species, which contributed to aggregated spatial patterns of their juveniles. Spatial patterns suggested associations between heterospecific palms experienced lower density-dependent mortality than associations between conspecifics and this likely contributes to the coexistence of the two palm species in their early life-history. These findings highlight the importance of dispersers to species coexistence and suggest over-hunting can lead to shifts away from species codominance. In chapter 3, I examined the contribution of dispersal, distance-and density-dependent to spatial ecology of Attalea phalerata. Using microsatellite-based parentage analysis, I found high levels of seed movement mediated by frugivore dispersers. Despite this, I found dispersal limitation remains strong enough to cause spatial aggregation between offspring and parents. As individuals grew towards maturity, distance and density dependent mortality contributed to increasingly disaggregated patterns between older offspring cohorts of parents, non-parent adults, and siblings. These results provide a foundation for assessing the impacts of hunting on the spatial ecology of palm populations. In chapter 4, we characterized 14 microsatellite loci for A. phalerata that were used in the parentage analysis of chapter 3. These loci amplified reliably and were sufficiently polymorphic and will be useful for future studies addressing population-level questions for this species. / text

<p>In this thesis, genetic methods for individual identification and sex determination of wolverines from non-invasive samples were developed and applied in genetic monitoring of Scandinavian wolverine populations. Paternity and mating system of wolverines were studied by combining genetic analysis with telemetry data. Moreover, the possibility to obtain DNA from claws left on tanned carnivore hides was investigated.</p><p>Non-invasive genetic sampling was effective in revealing important population parameters. For the subpopulation in southern Norway, a population size of approximately 90 individuals, an equal sex ratio and similar levels of genetic diversity as in the main Scandinavian population were revealed. Genetic erosion in this small population has likely been counteracted by immigration of individuals from the main population since its re-establishment around 1970.</p><p>During the 1990s, two areas in east-central Sweden were colonised by wolverines. In a survey comprising 400 non-invasive samples collected during five winters, a total of 22 wolverines were detected. Genetic data suggest that inbreeding has occurred in both areas and that the two populations were founded by as few as 2-4 individuals. These findings suggest that gene flow from the main population is crucial for their survival even in a short time perspective. The detection of occasional stray individuals from the main population shows that this is indeed feasible. </p><p>Paternity analysis of 145 wolverine offspring in northern Sweden and southern Norway confirmed a polygamous mating system in wolverines. Breeding pair formation was generally consistent with the territories held by males and females, i.e. breeding pairs had overlapping territories. In the majority of litters, siblings were assigned the same father, thus indicating that multiple paternity is rare. </p><p>Tanning is a common form of preservation of mammalian specimens that normally precludes genetic analysis. Nevertheless, I demonstrate the possibility to successfully extract and amplify DNA from claws left on tanned carnivore hides.</p>

In this thesis, genetic methods for individual identification and sex determination of wolverines from non-invasive samples were developed and applied in genetic monitoring of Scandinavian wolverine populations. Paternity and mating system of wolverines were studied by combining genetic analysis with telemetry data. Moreover, the possibility to obtain DNA from claws left on tanned carnivore hides was investigated. Non-invasive genetic sampling was effective in revealing important population parameters. For the subpopulation in southern Norway, a population size of approximately 90 individuals, an equal sex ratio and similar levels of genetic diversity as in the main Scandinavian population were revealed. Genetic erosion in this small population has likely been counteracted by immigration of individuals from the main population since its re-establishment around 1970. During the 1990s, two areas in east-central Sweden were colonised by wolverines. In a survey comprising 400 non-invasive samples collected during five winters, a total of 22 wolverines were detected. Genetic data suggest that inbreeding has occurred in both areas and that the two populations were founded by as few as 2-4 individuals. These findings suggest that gene flow from the main population is crucial for their survival even in a short time perspective. The detection of occasional stray individuals from the main population shows that this is indeed feasible. Paternity analysis of 145 wolverine offspring in northern Sweden and southern Norway confirmed a polygamous mating system in wolverines. Breeding pair formation was generally consistent with the territories held by males and females, i.e. breeding pairs had overlapping territories. In the majority of litters, siblings were assigned the same father, thus indicating that multiple paternity is rare. Tanning is a common form of preservation of mammalian specimens that normally precludes genetic analysis. Nevertheless, I demonstrate the possibility to successfully extract and amplify DNA from claws left on tanned carnivore hides.

Intensive aquaculture of Atlantic cod is fast developing in both Northern Europe and Canada. The last six years have seen major improvements in the larval rearing protocols and husbandry techniques for this species. Although breeding programmes are currently being developed by both governmental and private institutions in the main cod producing countries (i.e. Norway, Iceland and Canada), most hatcheries still rely on the mass spawning of their own broodstock. Mass spawning tanks are complex systems where fish are left to spawn naturally and fertilised eggs are collected with the overflowing water, with little or no control over the matings of the animals. Few published studies in other commercial marine species (i.e. turbot and sole) have attempted to analyse the output from such systems using microsatellite markers and several parentage analysis software programs. A review of these publications exposed a lack of consistency in the methods used to analyse such complex datasets. This problem was addressed by carrying out a detailed comparison of two analytical principals (i.e. assignment by strict exclusion and assignment by probabilities) and four parentage software programmes (i.e. FAP, VITASSIGN, CERVUS and PAPA), using the DNA profiles, at 5 loci, from 300 cod fry issued from the mass spawning of a large hatchery cod broodstock tank (consisting of 99 fish). This study revealed large discrepancies in the allocation outcomes between exclusion-based and probability-based assignments caused by the important rate of typing errors present in the dataset. Out of the four softwares tested, FAP (Taggart, 2007) was the most appropriate to use for handling such a dataset. It combined the most conservative method of assignment with the most informative output for the results displayed. In an attempt to study the breeding dynamics in a cod commercial hatchery, parental contributions to five groups of 300 fry (from five single days of spawning and from two commercial mass spawning cod tanks) were analysed, based on the genotyping data from eight loci. The parentage results from the exclusion-based analyses revealed that, on a single day, at least 25 to 30% of the total breeding population contributed to fertilised eggs that resulted in viable offspring at 50 and 83 days post-hatch. Family representations were highly skewed - with the marked dominance of a few males - and effective breeding populations were consistently low (approx. 5% of the total breeding population). Parental contribution to a group of 960 codlings - produced following intensive commercial practices (i.e. including successive size gradings and mixing of batches) and belonging to a single graded group - was also analysed, based on the genotyping data from eleven loci. The effective breeding population size of the juvenile batch (c. 14% of the total broodstock population) was two to three times greater than the effective size observed on a single day of mass spawning. The per-generation rate of inbreeding was however relatively high, for this batch alone, at 2.5%. Based on these results, suggestions were made to manage hatchery cod broodstock populations and implement genetic selection. Early maturation of farmed cod in sea cages (at two or three years old) is a major concern for ongrowers. Understanding the mechanism(s) behind sex determination in cod would probably help the development of a method to control sexual maturation. In an attempt to elucidate sex determination in cod, a protocol to induce gynogenesis was developed. Gynogenetic fish were successfully produced by irradiating cod milt with UV and applying a cold shock (at -6oC) to newly fertilised eggs. However, due to poor survival during larval rearing, only one gynogenetic fish survived long enough to be sexed; not enough to conclude anything on the sex determination mechanism(s) in cod.

L'évolution adaptative contribue probablement à l'adaptation des populations à des changements environnementaux rapides, l'observation empirique de nombreux cas d'évolution rapide dans les populations naturelles suivant de forts changements environnementaux abondant en ce sens. Dans cette thèse, je me suis concentrée sur l'estimation du potentiel évolutif d'une population naturelle de hêtre commun (Fagus sylvatica), une espèce à long cycle de vie, subissant des stress hydriques chroniques. Je considère ici une définition du potentiel évolutif dans le sens strict de la capacité d'une population à évoluer ; c'est donc un paramètre directement lié au taux d'évolution futur de la population considérée. Cette thèse a pour but d'apporter des éléments manquants concernant l'étude de l'adaptation chez les arbres, le rôle de l'évolution adaptative dans la capacité des arbres à composer avec les changements environnementaux futurs étant encore largement méconnu.La population étudiée montre un potentiel évolutif important, imputable à divers traits (principalement la phénologie du débourrement végétatif, et le Delta13C) qui présentent une diversité génétique élevée, sont soumis à une forte pression de sélection, et contribuent significativement à la valeur adaptative. Cette thèse appuie donc l'hypothèse selon laquelle l'évolution adaptative jouera un rôle important dans l'adaptation des arbres aux changements environnementaux futurs. Le rôle de la dispersion demeure incertain du fait d'une dispersion du pollen et des graines restreinte, mais également d'indices d'évènements de dispersion à longue distances favorisés par la présence de mortalité densité dépendante. / Adaptive evolution may promote populations' adaptation to rapid environmental changes which is sustained by recurrent empirical demonstrations of rapid adaptive evolution in the wild consecutively to strong environmental changes. In this PhD, I focused on the estimation of the in-situ evolutionary potential of a wild European beech (Fagus sylvatica) population, a long-lived tree species, undergoing chronic water stresses. I here considered the evolutionary potential in the strict sense of “evolvability” i.e. the ability of population to evolve; this parameter is thus directly linked to the rate of future adaptive evolution. This PhD aimed to fill a gap in tree adaptation studies, the role of adaptive evolution in tree populations' ability to cope with future environmental changes remaining largely unresolved.The studied a population displayed a high evolutionary potential because of a strong in-natura genetic variability of some traits and the relevance of these traits in trees adaptation, this PhD support the hypothesis that adaptive evolution is likely to play a key role in trees adaptation to future environmental changes. The role of dispersal remains unclear with apparently very restricted seed and pollen dispersal but also clues of long dispersal events promoted by the occurrence of density-dependent mortality.